Hello there, tcba2016.
Allow me to guide you through the whole process of making deposits in QuickBooks Desktop.
When you create an invoice and receive the payment, you'll need to choose Undeposited Funds as your Deposit to account. This way, you'll be able to select the right payment that you want to deposit.
Now you're ready to make deposit. I'd be delighted to guide you through the steps on how to do it.
You may also want to check out this article for your reference: Make Deposit.
That should do it. Please know that you're always welcome to post your concern or follow-up questions about making deposits. I'd be happy to help.